# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 17:17:53 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (3S)-3-[(2S,3R)-2-amino-3-hydroxybutyl]pyrrolidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](O)[C@@H](N)C[C@@H]1CCNC1=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 ECQ  ECQ  (3S)-3-[(2S,3R)-2-amino-3-hydroxybutyl]pyrrolidin-2-one  ligand  28  12  .  2021-08-08  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ECQ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 ECQ  OAD   O  O     0  -0.498   2.3808   1.9070   0.4904
 ECQ  CD2   C  C     0   0.569   2.2792   0.7172   0.2354
 ECQ  CG    C  CH1   0  -0.423   1.0526   0.0194  -0.3316
 ECQ  CD1   C  CH2   0  -0.463   1.3460  -1.4607  -0.0801
 ECQ  CAE   C  CH2   0  -0.259   2.8738  -1.5359  -0.0600
 ECQ  NAH   N  NH1   0  -0.630   3.2399  -0.2089   0.3877
 ECQ  CB    C  CH2   0  -0.421  -0.2536   0.5349   0.2523
 ECQ  CA    C  CH1   0  -0.115  -1.4880  -0.1487  -0.3512
 ECQ  N     N  NH2   0  -0.792  -1.5862  -0.0160  -1.7975
 ECQ  C     C  CH1   0   0.074  -2.7868   0.3744   0.2714
 ECQ  O     O  OH1   0  -0.676  -2.6616   0.2618   1.6769
 ECQ  CMK   C  CH3   0  -0.683  -4.0102  -0.3781  -0.2287
 ECQ  HN1   H  HNH2  0   0.338  -1.4691   0.9553  -2.0653
 ECQ  HN2   H  HNH2  0   0.352  -0.8358  -0.5221  -2.2486
 ECQ  HA    H  HCH1  0   0.226  -1.4333  -1.2226  -0.1328
 ECQ  HMK1  H  HCH3  0   0.225  -4.9196   0.0067   0.2384
 ECQ  HMK2  H  HCH3  0   0.231  -4.1182  -0.2739  -1.3061
 ECQ  HMK3  H  HCH3  0   0.217  -3.9340  -1.4427   0.0035
 ECQ  HB1   H  HCH2  0   0.233  -0.2370   0.3870   1.3344
 ECQ  HB2   H  HCH2  0   0.223  -0.3251   1.6149   0.0841
 ECQ  HG    H  HCH1  0   0.266   1.0782   0.2188  -1.4118
 ECQ  HAH   H  HNH1  0   0.395   4.1846   0.0381   0.6390
 ECQ  HAE1  H  HCH2  0   0.250   3.2490  -2.2983   0.6220
 ECQ  HAE2  H  HCH2  0   0.235   3.2804  -1.7448  -1.0537
 ECQ  HD11  H  HCH2  0   0.244   0.9475  -1.7540   0.8944
 ECQ  HD12  H  HCH2  0   0.253   0.9140  -2.1235  -0.8285
 ECQ  H     H  HCH1  0   0.183  -2.8895   1.4340  -0.0155
 ECQ  HO    H  HOH1  0   0.449  -3.4743   0.5866   2.0759

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 ECQ  OAD  CD2   double  1.221  0.020  1.221
 ECQ  CD2  CG    single  1.521  0.020  1.521
 ECQ  CD2  NAH   single  1.343  0.020  1.343
 ECQ  CG   CB    single  1.521  0.020  1.521
 ECQ  CG   HG    single  0.970  0.020  1.090
 ECQ  CG   CD1   single  1.530  0.020  1.530
 ECQ  CD1  CAE   single  1.530  0.020  1.530
 ECQ  CD1  HD11  single  0.970  0.020  1.090
 ECQ  CD1  HD12  single  0.970  0.020  1.090
 ECQ  CAE  NAH   single  1.448  0.020  1.448
 ECQ  CAE  HAE1  single  0.970  0.020  1.090
 ECQ  CAE  HAE2  single  0.970  0.020  1.090
 ECQ  NAH  HAH   single  0.860  0.020  1.020
 ECQ  CB   CA    single  1.535  0.020  1.535
 ECQ  CB   HB1   single  0.970  0.020  1.090
 ECQ  CB   HB2   single  0.970  0.020  1.090
 ECQ  CA   N     single  1.456  0.020  1.456
 ECQ  CA   HA    single  0.970  0.020  1.090
 ECQ  CA   C     single  1.532  0.020  1.532
 ECQ  N    HN1   single  0.890  0.020  1.040
 ECQ  N    HN2   single  0.890  0.020  1.040
 ECQ  C    O     single  1.416  0.020  1.416
 ECQ  C    CMK   single  1.521  0.020  1.521
 ECQ  C    H     single  0.970  0.020  1.090
 ECQ  O    HO    single  0.850  0.020  0.980
 ECQ  CMK  HMK1  single  0.970  0.020  1.090
 ECQ  CMK  HMK2  single  0.970  0.020  1.090
 ECQ  CMK  HMK3  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 ECQ  NAH   CD2  CG    107.63  3.000
 ECQ  NAH   CD2  OAD   126.06  3.000
 ECQ  CG    CD2  OAD   126.31  3.000
 ECQ  HG    CG   CB    109.63  3.000
 ECQ  HG    CG   CD1   109.44  3.000
 ECQ  CB    CG   CD1   115.44  3.000
 ECQ  CD1   CG   CD2   103.18  3.000
 ECQ  HG    CG   CD2   105.34  3.000
 ECQ  CB    CG   CD2   113.21  3.000
 ECQ  HD12  CD1  HD11  107.75  3.000
 ECQ  HD12  CD1  CAE   112.04  3.000
 ECQ  HD11  CD1  CAE   109.84  3.000
 ECQ  HD12  CD1  CG    113.56  3.000
 ECQ  HD11  CD1  CG    109.65  3.000
 ECQ  CAE   CD1  CG    103.96  3.000
 ECQ  HAE2  CAE  HAE1  107.88  3.000
 ECQ  HAE2  CAE  NAH   111.23  3.000
 ECQ  HAE1  CAE  NAH   111.14  3.000
 ECQ  HAE2  CAE  CD1   111.64  3.000
 ECQ  HAE1  CAE  CD1   112.74  3.000
 ECQ  NAH   CAE  CD1   102.22  3.000
 ECQ  HAH   NAH  CAE   122.59  3.000
 ECQ  HAH   NAH  CD2   121.98  3.000
 ECQ  CAE   NAH  CD2   114.59  3.000
 ECQ  HB2   CB   HB1   106.65  3.000
 ECQ  HB2   CB   CA    109.05  3.000
 ECQ  HB1   CB   CA    109.97  3.000
 ECQ  HB2   CB   CG    109.35  3.000
 ECQ  HB1   CB   CG    108.75  3.000
 ECQ  CA    CB   CG    112.89  3.000
 ECQ  HA    CA   C     107.18  3.000
 ECQ  C     CA   N     108.38  3.000
 ECQ  HA    CA   N     106.88  3.000
 ECQ  C     CA   CB    111.71  3.000
 ECQ  HA    CA   CB    108.52  3.000
 ECQ  N     CA   CB    113.85  3.000
 ECQ  HN2   N    HN1   106.01  3.000
 ECQ  HN2   N    CA    110.34  3.000
 ECQ  HN1   N    CA    109.99  3.000
 ECQ  H     C    CMK   108.36  3.000
 ECQ  H     C    O     110.06  3.000
 ECQ  CMK   C    O     111.00  3.000
 ECQ  H     C    CA    107.53  3.000
 ECQ  CMK   C    CA    112.29  3.000
 ECQ  O     C    CA    107.53  3.000
 ECQ  HO    O    C     108.07  3.000
 ECQ  HMK3  CMK  HMK2  108.11  3.000
 ECQ  HMK3  CMK  HMK1  108.09  3.000
 ECQ  HMK2  CMK  HMK1  107.89  3.000
 ECQ  HMK3  CMK  C     110.87  3.000
 ECQ  HMK2  CMK  C     110.99  3.000
 ECQ  HMK1  CMK  C     110.78  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 ECQ  CONST_01  CAE  NAH  CD2  CG     0.00   0.0  0
 ECQ  CONST_02  CAE  NAH  CD2  OAD  180.00   0.0  0
 ECQ  CONST_03  HAH  NAH  CD2  CG   180.00   0.0  0
 ECQ  Var_01    CD1  CAE  NAH  CD2  -19.48  30.0  1
 ECQ  Var_02    NAH  CAE  CD1  CG    27.85  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 ECQ  chir_01  CG  CD2  CB  CD1  positiv
 ECQ  chir_02  CA  N    C   CB   positiv
 ECQ  chir_03  C   O    CA  CMK  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 ECQ  plan-1  OAD  0.020
 ECQ  plan-1  CD2  0.020
 ECQ  plan-1  CG   0.020
 ECQ  plan-1  CAE  0.020
 ECQ  plan-1  NAH  0.020
 ECQ  plan-1  HAH  0.020

